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Complete Summary Experimental Cell Biology 1

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  • Course
  • Experimental Cell Biology 1 (AB_1047)
  • Institution
  • Vrije Universiteit Amsterdam (VU)
  • Book
  • Essential Cell Biology

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  • June 23, 2021
  • 90
  • 2020/2021
  • Class notes
  • D.bald
  • All classes

Subjects

  • experimental cell biology
  • research
  • membranes
  • experimental
  • bacteria
  • cells
  • techniques

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  • Experimental Cell Biology 1 (AB_1047)
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ECB 1 – HC 1- The basics
The cell (from Latin cella, meaning "small room") is the basic structural, functional, and biological
unit of all known organisms. A cell is the smallest unit of life. Cells are often called the "building
blocks of life". The study of cells is called cell biology, cellular biology, or cytology. Cells come in
different shapes and sizes but they all share common properties.
Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such
as proteins and nucleic acids. They have their own metabolism and can regulate their growth and
division. They also tesponse to environmental signals, internal and external communication. Most
plant and animal cells are only visible under a microscope, with dimensions between 1 and 100
micrometers. Organisms can be classified as unicellular (consisting of a single cell such as
bacteria) or multicellular (including plants and animals). Most unicellular organisms are classed as
microorganisms.

Cell biology (also cellular biology or cytology) is a branch of biology studying the structure and
function of the cell, also known as the basic unit of life. Cell biology encompasses both prokaryotic
and eukaryotic cells and can be divided into many sub-topics which may include the study of cell
metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells
is performed using several techniques such as cell culture, various types of microscopy, and cell
fractionation. These have allowed for and are currently being used for discoveries and research
pertaining to how cells function, ultimately giving insight into understanding larger organisms.
Knowing the components of cells and how cells work is fundamental to all biological sciences while
also being essential for research in biomedical fields such as cancer, and other diseases. Research
in cell biology is interconnected to other fields such as genetics, molecular genetics, biochemistry,
molecular biology, medical microbiology, immunology, and cytochemistry.
All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, regulates what
moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the
membrane, the cytoplasm takes up most of the cell's volume. All cells (except red blood cells which
lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess
DNA, the hereditary material of genes, and RNA, containing the information necessary to build
various proteins such as enzymes. Building proteins from DNA is seen as the cell's primary
machinery. There are also other kinds of biomolecules in cells, called metabolites (molecules
produced or altered by cells).
The central dogma of molecular biology is an explanation of the flow of genetic information
within a biological system. It is often stated as "DNA makes RNA, and RNA makes protein". The
central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential
information. It states that such information cannot be transferred back from protein to either protein
or nucleic acid. A second version of the central dogma is popular but incorrect. Nowadays it is
stated that interplay between these factors are very important.

,Prokaryotic cells

Structure of a typical prokaryotic cell
Prokaryotes include bacteria and archaea, two of the
three domains of life. Prokaryotic cells were the first
form of life on Earth, characterized by having vital
biological processes including cell signaling
(Lectures: Two-component systems and
Membranes as borderlines). They are simpler and
smaller than eukaryotic cells, and lack a nucleus,
and other membrane-enclosed
organelles/compartments. The DNA of a prokaryotic
cell consists of a single circular chromosome that is
in direct contact with the cytoplasm. The nuclear
region in the cytoplasm is called the nucleoid. Most
prokaryotes are the smallest of all organisms
ranging from 1-5µm in diameter. Prokaryotic cells
are biochemically flexible.
A prokaryotic cell has three regions:

• Enclosing the cell is the cell envelope, generally consisting of a plasma membrane covered
by a cell wall which, for some bacteria, may be further covered by a third layer called a
capsule. Though most prokaryotes have both a cell membrane and a cell wall, there are
exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea) which only
possess the cell membrane layer. The envelope gives rigidity to the cell and separates the
interior of the cell from its environment, serving as a protective filter. The cell wall consists
of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It
also prevents the cell from expanding and bursting (cytolysis) from osmotic pressure due
to a hypotonic environment. Some eukaryotic cells (plant cells and fungal cells) also have
a cell wall.

• Inside the cell is the cytoplasmic region that contains the genome (DNA), ribosomes and
various sorts of inclusions. The genetic material is freely found in the cytoplasm.
Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are
usually circular. Linear bacterial plasmids have been identified in several species of
spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi,
which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a
nucleoid. Plasmids encode additional genes, such as antibiotic resistance genes.


• On the outside, flagella and pili project from the cell's surface. These are structures (not
present in all prokaryotes) made of proteins that facilitate movement and communication
between cells.

,Eukaryotic cells

Plants, animals, fungi, slime moulds,
protozoa, and algae are all eukaryotic.
These cells are larger than a typical
prokaryote (20-50µm) and can be as much
as a thousand times greater in volume. The
main distinguishing feature of eukaryotes as
compared to prokaryotes is
compartmentalization: the presence of
membrane-bound organelles
(compartments) in which specific activities
take place. Most important among these is a
cell nucleus, an organelle that houses the
cell's DNA. This nucleus gives the eukaryote
its name, which means "true kernel
(nucleus)". Other differences include:

• The plasma membrane resembles that of prokaryotes in function, with minor differences in
the setup. Cell walls may or may not be present.

• The eukaryotic DNA is organized in one or more linear molecules, called chromosomes,
which are associated with histone proteins. All chromosomal DNA is stored in the cell
nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such
as mitochondria also contain some DNA.

• Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in
chemosensation, mechanosensation, and thermosensation. Each cilium may thus be
"viewed as a sensory cellular antennae that coordinates a large number of cellular signaling
pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division
and differentiation."

• Motile eukaryotes can move using motile cilia or flagella. Motile cells are absent in conifers
and flowering plants. Eukaryotic flagella are more complex than those of prokaryotes.


Eukaryotic cells

• Cell nucleus: A cell's information center, the cell nucleus is the most conspicuous organelle
found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost
all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and
separated from the cytoplasm by a double membrane called the nuclear envelope. The
nuclear envelope isolates and protects a cell's DNA from various molecules that could
accidentally damage its structure or interfere with its processing. During processing, DNA
is transcribed, or copied into a special RNA,
called messenger RNA (mRNA). This mRNA
is then transported out of the nucleus, where it
is translated into a specific protein molecule.
The nucleolus is a specialized region within the
nucleus where ribosome subunits are
assembled. It is thought that the nucleolus is
also involved in protein quality control. In
prokaryotes, DNA processing takes place in
the cytoplasm.

, • Mitochondria and Chloroplasts: generate energy for the cell. Mitochondria are self-
replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of
all eukaryotic cells. Respiration occurs in the cell mitochondria, which generate the cell's
energy by oxidative phosphorylation, using oxygen to release energy stored in cellular
nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by binary
fission, like prokaryotes. Experiments showed that the Endoplasmic reticulum may be
responsible for the division of mitochondria. Chloroplasts can only be found in plants and
algae, and they capture the sun's energy to make carbohydrates through photosynthesis.

• The cytosol: In the eukaryotic cell, the cytosol is surrounded by the cell membrane and is
part of the cytoplasm, which also comprises the mitochondria, plastids, and other
organelles (but not their internal fluids and structures); the cell nucleus is separate. The
cytosol is thus a liquid matrix around the organelles. In prokaryotes, most of the chemical
reactions of metabolism take place in the cytosol, while a few take place in membranes or
in the periplasmic space. In eukaryotes, while many metabolic pathways still occur in the
cytosol, others take place within organelles.

The cytosol is a complex mixture of substances dissolved in water. Although water forms
the large majority of the cytosol, its structure and properties within cells is not well
understood. The concentrations of ions such as sodium and potassium are different in the
cytosol than in the extracellular fluid; these differences in ion levels are important in
processes such as osmoregulation, cell signaling, and the generation of action potentials
in excitable cells such as endocrine, nerve and muscle cells. The cytosol also contains
large amounts of macromolecules, which can alter how molecules behave, through
macromolecular crowding.
Diagram of the endomembrane system

• Endoplasmic reticulum: The endoplasmic reticulum (ER) is a transport network for
molecules targeted for certain modifications and specific destinations (First station for
secreted proteins), as compared to molecules that float freely in the cytoplasm. The ER
has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into
the ER, and the smooth ER, which lacks ribosomes. The smooth ER plays a role in calcium
sequestration and release.

• Golgi apparatus: The primary function of the Golgi apparatus is to process and package
the macromolecules such as proteins and lipids that are synthesized by the cell.
Modification, in particular glycosylation occurs in the Golgi to sort the newly synthesized
proteins.There are various mechanisms for glycosylation, although most share several
common features:

o Glycosylation, unlike glycation, is an enzymatic process. Indeed, glycosylation is
thought to be the most complex post-translational modification, because of the large
number of enzymatic steps involved.
o The donor molecule is often an activated nucleotide sugar.
o The process is non-templated (unlike DNA transcription or protein translation);
instead, the cell relies on segregating enzymes into different cellular compartments.
Therefore, glycosylation is a site-specific modification.

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